[gmx-users] some problems by freshman

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 16 10:33:56 CEST 2002

On Fri, 2002-08-16 at 10:27, zpxu wrote:
> Dear All:
>     I am wondering if you can show me such fundamental things:
> 1) I want L-J interaction only between the C_I(innertube) and C_O(outertube)
> atoms (two type of atoms in one molecule).
>     and their are four sections concern L-J potential.
>     a)section [atomtypes] in topology file
>     b)section [nonbond_params] in topology file
>     c)section [pairtypes] in topology file
>     d)section [pairs] in topology file
>     now I only use b).
>     is it ok?
You must define the atom types in a), but you can set the parameters in
b) if you like.

> 2) the unit of potential parameters, I use nm,kJ/mol
>     is it ok?

> 3) my coordinate is at nanometer scale, so I shift it by 3nm, let the tubes
> in box.

> 4) I set charge to zero, and set charge group arbitrarily.will it be ok?
Set them all to the atom number
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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